Mercurial > repos > proteore > proteore_filter_keywords_values

comparison filter_kw_val.xml @ 7:5621406a4d2f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty
author proteore
date Fri, 28 Jun 2019 05:09:20 -0400
parents b4641c0f8a82
children 98cb671a92eb
comparison
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6:b4641c0f8a82 7:5621406a4d2f
1 <tool id="MQoutputfilter" name="Filter by keywords and/or numerical value" version="2019.03.11"> 1 <tool id="MQoutputfilter" name="Filter by keywords and/or numerical value" version="2019.06.27">
2 <description></description> 2 <description></description>
3 <requirements> 3 <requirements>
4 </requirements> 4 </requirements>
5 <stdio> 5 <stdio>
6 <exit_code range="1:" /> 6 <exit_code range="1:" />
57 57
58 <repeat name="keyword" title="Filter by keywords" > 58 <repeat name="keyword" title="Filter by keywords" >
59 <param name="ncol" type="text" value="c1" label="Column number on which to apply the filter" help='For example, fill in "c1" if you want to seek keywords in the first column (and keep or discard them)'> 59 <param name="ncol" type="text" value="c1" label="Column number on which to apply the filter" help='For example, fill in "c1" if you want to seek keywords in the first column (and keep or discard them)'>
60 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator> 60 <validator type="regex" message="Please enter a column number, for example: 'c1' for the first column">[c]{0,1}[0-9]+</validator>
61 </param> 61 </param>
62 <param type="boolean" name="match" truevalue="True" label="Search for exact match?" help='Choosing "Yes" will only filter out exact match (e.g. case sensitive), see help section' /> 62 <param type="boolean" name="match" truevalue="True" label="Search for exact match?" help='Choosing "Yes" will only filter out exact match, see help section' />
63 <conditional name="k" > 63 <conditional name="k" >
64 <param name="kw" type="select" label="Enter keywords" > 64 <param name="kw" type="select" label="Enter keywords" >
65 <option value="text" selected="true">copy/paste</option> 65 <option value="text" selected="true">copy/paste</option>
66 <option value="file">File containing keywords</option> 66 <option value="file">File containing keywords</option>
67 </param> 67 </param>
116 </when> 116 </when>
117 <when value="false"/> 117 <when value="false"/>
118 </conditional> 118 </conditional>
119 </inputs> 119 </inputs>
120 <outputs> 120 <outputs>
121 <data name="discarded_lines" format="tsv" label="Filtered_${input1.name} - discarded_lines" />
121 <data name="kept_lines" format="tsv" label="Filtered_${input1.name}" /> 122 <data name="kept_lines" format="tsv" label="Filtered_${input1.name}" />
122 <data name="discarded_lines" format="tsv" label="Filtered_${input1.name} - discarded_lines" />
123 </outputs> 123 </outputs>
124 <tests> 124 <tests>
125 <test> 125 <test>
126 <param name="input1" value="Lacombe_et_al_2017_OK.txt" /> 126 <param name="input1" value="Lacombe_et_al_2017_OK.txt" />
127 <param name="header" value="true" /> 127 <param name="header" value="true" />
197 197
198 ALDOA_RABBIT 198 ALDOA_RABBIT
199 199
200 LYSO_ECOLI 200 LYSO_ECOLI
201 201
202 Lines that contains these keywords will be removed from input file. 202 Lines that contains these keywords will be either removed (if "Discard" selected) or retained (if "Keep" selected) from input file.
203 203
204 "Search for exact match?": Keywords search can be applied by performing either exact match or partial one by using the following option: 204 "Search for exact match?": Keywords search can be applied by performing either exact match or partial one by using the following option:
205 205
206 - If you choose **Yes**, only the fields that contains exactly the same content will be removed (i.e. using the "discard" mode). 206 - If you choose **Yes**, only the fields that contains exactly the same content will be removed (i.e. using the "discard" mode).
207 207
208 - If you choose **No**, all the fields containing the keyword will be removed. 208 - If you choose **No**, all the fields containing the keyword will be removed.
209 209
210 For both options, the filter is case insensitive (uppercase and lowercase are treated equally)
211
210 Example: 212 Example:
211 213
212 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly the word "kinase" will be removed. 214 **Yes** option (exact match) selected using the keyword "kinase": only lines which contain exactly the word "kinase" will be removed.
213 215
214 **No** option (partial match) for "kinase": lines which contain "kinase" and lines with "alpha-kinase" (and so on) will be removed. 216 **No** option (partial match) for "kinase": lines which contain "kinase" and lines with "alpha-kinase" (and so on) will be removed.
217
215 218
216 ----- 219 -----
217 220
218 **Filter by numerical values**: You can filter your data by a column of numerical values. 221 **Filter by numerical values**: You can filter your data by a column of numerical values.
219 222
255 258
256 .. class:: infomark 259 .. class:: infomark
257 260
258 **Authors** 261 **Authors**
259 262
260 David Christiany, T.P. Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR 263 David Christiany, Lien Nguyen, Florence Combes, Yves Vandenbrouck - CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
261 264
262 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR 265 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux - INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
263 266
264 This work has been partially funded through the French National Agency for Research (ANR) IFB project. 267 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
265 268
266 Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. 269 Help: contact@proteore.org for any questions or concerns about this tool.
267 270
268 ]]></help> 271 ]]></help>
269 <citations> 272 <citations>
270 </citations> 273 </citations>
271 </tool> 274 </tool>